Schema for ncbiRefSeqPredicted
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Database: oviAri4 Primary Table: ncbiRefSeqPredicted Row Count: 48,734   Data last updated: 2021-02-10
Format description: A gene prediction with some additional info. On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 585 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
name | XR_001433683.1 | varchar(255) | values | Name of gene (usually transcript_id from GTF) |
chrom | chr1 | varchar(255) | values | Reference sequence chromosome or scaffold |
strand | + | char(1) | values | + or - for strand |
txStart | 49236 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
txEnd | 54549 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
cdsStart | 54549 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
cdsEnd | 54549 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
exonCount | 3 | int(10) unsigned | range | Number of exons |
exonStarts | 49236,52670,54487, | longblob | | Exon start positions (or end positions for minus strand item) |
exonEnds | 49423,52819,54549, | longblob | | Exon end positions (or start positions for minus strand item) |
score | 0 | int(11) | range | score |
name2 | LOC106990386 | varchar(255) | values | Alternate name (e.g. gene_id from GTF) |
cdsStartStat | none | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS start annotation (none, unknown, incomplete, or complete) |
cdsEndStat | none | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS end annotation (none, unknown, incomplete, or complete) |
exonFrames | -1,-1,-1, | longblob | | Reading frame of the start of the CDS region of the exon, in the direction of transcription (0,1,2), or -1 if there is no CDS region. |
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Connected Tables and Joining Fields
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Sample Rows
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bin | name | chrom | strand | txStart | txEnd | cdsStart | cdsEnd | exonCount | exonStarts | exonEnds | score | name2 | cdsStartStat | cdsEndStat | exonFrames |
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585 | XR_001433683.1 | chr1 | + | 49236 | 54549 | 54549 | 54549 | 3 | 49236,52670,54487, | 49423,52819,54549, | 0 | LOC106990386 | none | none | -1,-1,-1, |
585 | XM_015091617.1 | chr1 | - | 72196 | 75389 | 72196 | 75389 | 14 | 72196,72348,72453,72560,72629,72675,73024,73120,73153,73350,73422,73526,73564,75151, | 72347,72451,72558,72628,72674,73023,73118,73151,73349,73420,73524,73562,73585,75389, | 0 | RTP5 | cmpl | cmpl | 2,1,1,2,2,2,1,0,2,1,1,1,1,0, |
585 | XM_012176227.2 | chr1 | + | 83055 | 90946 | 83151 | 90578 | 3 | 83055,89481,90162, | 83227,89844,90946, | 0 | PDCD1 | cmpl | cmpl | 0,1,1, |
585 | XM_015091618.1 | chr1 | - | 108743 | 127241 | 108743 | 127241 | 5 | 108743,110013,110200,111339,127100, | 109508,110199,110278,111426,127241, | 0 | GAL3ST2 | cmpl | cmpl | 0,0,0,0,0, |
586 | XM_012105914.2 | chr1 | - | 133788 | 158785 | 134596 | 156296 | 11 | 133788,143541,145570,146732,147795,148720,149007,150262,151670,155938,158158, | 134856,143707,145713,146813,148082,148841,149580,150402,151728,156306,158785, | 0 | D2HGDH | cmpl | cmpl | 1,0,1,1,2,1,1,2,1,0,-1, |
586 | XM_015091619.1 | chr1 | - | 164261 | 176934 | 164522 | 176934 | 10 | 164261,165630,168021,168668,169003,169260,170694,170794,176082,176901, | 164565,165823,168127,168788,169098,169372,170792,170860,176242,176934, | 0 | ING5 | cmpl | cmpl | 2,1,0,0,1,0,1,1,0,0, |
586 | XM_004003428.3 | chr1 | + | 185584 | 192779 | 185606 | 192633 | 6 | 185584,186740,188824,190296,192523,192607, | 185736,186849,188915,190494,192605,192779, | 0 | DTYMK | cmpl | cmpl | 0,1,2,0,0,1, |
586 | XM_015091620.1 | chr1 | - | 197895 | 212123 | 198049 | 212013 | 13 | 197895,198450,199407,199498,199706,200069,202425,202997,203352,203830,204995,205194,212003, | 198190,198507,199497,199554,199785,200263,202505,203090,203470,203929,205067,205296,212123, | 0 | ATG4B | cmpl | cmpl | 0,0,0,1,0,1,2,2,1,1,1,1,0, |
586 | XM_015091621.1 | chr1 | + | 212656 | 248024 | 212656 | 247887 | 7 | 212656,212999,214630,215117,234191,235349,247767, | 212898,213449,215116,215800,234356,235513,248024, | 0 | THAP4 | cmpl | cmpl | 0,2,2,2,1,1,0, |
586 | XR_001039844.1 | chr1 | + | 251676 | 254780 | 254780 | 254780 | 2 | 251676,253227, | 252023,254780, | 0 | LOC105612006 | none | none | -1,-1, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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